User: Rory Stark

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Rory Stark2.8k
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CRUK, Cambridge, UK
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r*********@cruk.cam.ac.uk

I am Principal Scientist, Computational Biology at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

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Answer: A: Error in DBA_OLAP_RATE
... Two issues here. In the first example (`mask=broad_gtsf1$masks$Mutant & broad_gtsf1$masks$WT`), there are no peaksets that are *both* Mutant **and** WT: > sum(broad_gtsf1$masks$Mutant & broad_gtsf1$masks$WT) [1] 0 You should use | (or) -- peaks that are *either* Mutant **or** W ...
written 9 days ago by Rory Stark2.8k
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Answer: A: DiffBind returns empty consensus peakset
... This is showing that zero sites have been loaded. One unusual thing I see is that your use of `system.file()` to specify the peaks directories. As you are giving full paths to the peaks (starting with `"/home"`), you shouldn't need to use `system.file()` and specify them as being installed with the ...
written 13 days ago by Rory Stark2.8k
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Answer: A: Reading peaks from MACS2 with DiffBind
... You can read in *narrowPeak* files by setting the `PeakCaller` to `"narrow"` in the sample sheet. Alternatively, you can read in the *xls* files created by **MACS2** by setting the `PeakCaller` to `"macs"`. -Rory ...
written 20 days ago by Rory Stark2.8k
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Answer: A: DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from
... I'm not sure who is saying that you "should expect that the blue density plot is symmetrical around the X axis (when my data is properly normalized)". While this tends to be true for RNA-seq, in ChIP-seq there can be radical shifts in binding levels between conditions (depending on your treatments). ...
written 20 days ago by Rory Stark2.8k
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Answer: A: Diffbind affinity based analysis
... It is most certainly possible for the quantitative (affinity) analysis to be unable to identify differentially bound sites, even when there are peaks called only in one condition. There are a number of reasons why this can occur. First, there may be a number of borderline peaks that are above the ...
written 28 days ago by Rory Stark2.8k
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Answer: A: Can I input peak files from Genrich as input reads in DiffBind?
... Yes, this should work with the `.narrowPeak` files. In the sample sheet, the values in the `PeakCaller` column should be set to `"narrow"`. ...
written 12 weeks ago by Rory Stark2.8k
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Comment: C: How to produce the fraction of reads in peaks (FRiP) using DiffBind
... > atac <- dba(sampleSheet = "atac.csv", bRemoveM = TRUE, bRemoveRandom = FALSE, bCorPlot = TRUE, peakFormat = "narrow") > dba.save(atac,"atac_peaks") > atac <- dba.count(atac, minOverlap = 1) > dba.save(atac,"atac_counts") which will create ...
written 12 weeks ago by Rory Stark2.8k
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Answer: A: Using DiffBind with only a counts table?
... You can import count data directly into DiffBind using the `Counts` column in the sample sheet. This is documented in the help page for dba.peakset(). It assume you have already generated a consensus peakset (same intervals for each sample) and counted the reads in each interval, so that you have a ...
written 12 weeks ago by Rory Stark2.8k
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Answer: A: How to produce the fraction of reads in peaks (FRiP) using DiffBind
... Hmmn, for some reason the `FRiP` values are not being computed by `dba.count()`, or else they would have shown up then you listed the DBA object `atac` after counting. If you can send me copies of the DBA object `atac` before and after the call to `dba,count()` (or a link where I can download them), ...
written 12 weeks ago by Rory Stark2.8k
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Answer: A: DiffBind peaks input file format
... In the `summit.bed` files, the intervals are all only one base wide, while in the `.xls` file, the peaks are much wider and of variable width. As the pre-counting correlations are based on overlaps, there will be very little overlap when using `summit.bed` files. This same problem will limit the num ...
written 3 months ago by Rory Stark2.8k

Latest awards to Rory Stark

Popular Question 7 months ago, created a question with more than 1,000 views. For diffbind
Scholar 7 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 8 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Differential analysis of multiple samples with different time points
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: diffbind finding not differential site
Scholar 8 months ago, created an answer that has been accepted. For A: DiffBind differential binding normalization with different levels of binding
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 9 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 13 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Commentator 24 months ago, created a comment with at least 3 up-votes. For C: Diffbind - What exactly is a "consensus" peak set?
Scholar 24 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 24 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Popular Question 24 months ago, created a question with more than 1,000 views. For diffbind
Popular Question 24 months ago, created a question with more than 1,000 views. For DiffBind Question
Popular Question 24 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 24 months ago, created an answer that has been accepted. For A: DiffBind MA plot
Scholar 24 months ago, created an answer that has been accepted. For A: DiffBind dba.analyze() to return all differentially enriched peaks?
Scholar 24 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 24 months ago, created an answer that has been accepted. For A: Diffbind and dba.peakset vs dba.overlap
Scholar 24 months ago, created an answer that has been accepted. For A: DiffBind - Losing replicate information?
Scholar 24 months ago, created an answer that has been accepted. For A: Diffbind: dba.plot retrieve variance explained
Scholar 24 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 24 months ago, created an answer that has been accepted. For A: DiffBind Heatmap Omitting Results?
Popular Question 24 months ago, created a question with more than 1,000 views. For minOverlap in DiffBind in R- what does it mean?
Scholar 24 months ago, created an answer that has been accepted. For A: Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind

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